How To Install iqtree on Debian 10
Introduction
In this tutorial we learn how to install iqtree
on Debian 10.
What is iqtree
iqtree is:
IQ-TREE is a very efficient maximum likelihood phylogenetic software with following key features among others:
- A novel fast and effective stochastic algorithm to estimate maximum likelihood trees. IQ-TREE outperforms both RAxML and PhyML in terms of likelihood while requiring similar amount of computing time (see Nguyen et al., 2015)
- An ultrafast bootstrap approximation to assess branch supports (see Minh et al., 2013).
- A wide range of substitution models for binary, DNA, protein, codon, and morphological alignments.
- Ultrafast model selection for all data types, 10 to 100 times faster than jModelTest and ProtTest.
- Finding best partition scheme like PartitionFinder.
- Partitioned models with mixed data types for phylogenomic (multi- gene) alignments, allowing for separate, proportional, or joint branch lengths among genes.
- Supporting the phylogenetic likelihod library (PLL) (see Flouri et al., 2014)
There are three methods to install iqtree
on Debian 10. We can use apt-get
, apt
and aptitude
. In the following sections we will describe each method. You can choose one of them.
Install iqtree Using apt-get
Update apt database with apt-get
using the following command.
sudo apt-get update
After updating apt database, We can install iqtree
using apt-get
by running the following command:
sudo apt-get -y install iqtree
Install iqtree Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install iqtree
using apt
by running the following command:
sudo apt -y install iqtree
Install iqtree Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Debian. Update apt database with aptitude
using the following command.
sudo aptitude update
After updating apt database, We can install iqtree
using aptitude
by running the following command:
sudo aptitude -y install iqtree
How To Uninstall iqtree on Debian 10
To uninstall only the iqtree
package we can use the following command:
sudo apt-get remove iqtree
Uninstall iqtree And Its Dependencies
To uninstall iqtree
and its dependencies that are no longer needed by Debian 10, we can use the command below:
sudo apt-get -y autoremove iqtree
Remove iqtree Configurations and Data
To remove iqtree
configuration and data from Debian 10 we can use the following command:
sudo apt-get -y purge iqtree
Remove iqtree configuration, data, and all of its dependencies
We can use the following command to remove iqtree
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge iqtree
Dependencies
iqtree have the following dependencies:
References
Summary
In this tutorial we learn how to install iqtree
package on Debian 10 using different package management tools: apt
, apt-get
and aptitude
.